After leaving The Saddletramps, Harmer put together a band of her own with several Kingston, Ontario musicians, and settled on the name Weeping Tile.[2] The band released its first independent cassette in 1994. Soon afterward, they signed to a major label, and the cassette was re-released in 1995 as Eepee. The band quickly became a popular draw on the rock club circuit and on campus radio with their subsequent albums, but never broke through to the mainstream, and broke up in 1998 after being dropped from their label.[3]

Also in 1998, Harmer recorded a set of pop standards as a Christmas gift for her father.[2] After hearing it, her friends and family convinced her to release it as an album, and in 1999 she released it independently as Songs for Clem.[2] Harmer quickly began working on another album, and in 2000, she released You Were Here.[3]

A poppier, more laid-back effort than her work with Weeping Tile, You Were Here became Harmer's mainstream breakthrough, spawning the hits "Basement Apartment" and "Don't Get Your Back Up". The album also appeared on many critics' year-end lists, including TIME magazine, which called it the year's best debut album. It was eventually certified platinum for sales of 100,000 copies in Canada. Almost half of the album (including both of its major hits) consisted of songs she had previously recorded with Weeping Tile or The Saddletramps.

In 2002, her song "Silver Road" was featured as the lead track of the soundtrack of the film Men With Brooms.

In 2004, she released All of Our Names. The album included the singles "Almost", which made the top 20 on Canadian pop charts, and "Pendulums".

Her fourth album, I'm a Mountain, was released in Canada on November 8, 2005 and in the United States in February 2006. It was nominated for the 2006 Polaris Music Prize, a jury-selected $20,000 cash prize for the Canadian album of the year.

In February 2007, Harmer received three Juno Award nominations. I'm a Mountain was up for Best Adult Alternative Album and her DVD Escarpment Blues was up for Best Music DVD. Harmer herself was also up for Songwriter of the Year for her work on "I Am Aglow", "Oleander" and "Escarpment Blues".

In 2010, Harmer released a fifth album, Oh Little Fire, which was nominated for three Juno Awards. The album signaled a shift toward a more rock-based sound.[5]

In 2005, Harmer co-founded PERL (Protecting Escarpment Rural Land), an organization which campaigned to protect the Niagara Escarpment from a proposed gravel development which would see some parts of wilderness near the escarpment removed.[9] To support the organization, she and her acoustic band embarked on a tour of the escarpment, hiking the Bruce Trail and performing at theatres and community halls in towns along the way. A documentary DVD of this tour was released in 2006 as Escarpment Blues. Harmer also coauthored a book about the campaign, The Last Stand : A Journey Through the Ancient Cliff-Face Forest of the Niagara Escarpment, which was published in 2007. In October 2012, PERL won their case against the development.

Harmer has performed and canvassed in support of the NDP and Marilyn Churley, her friend in the fight for the protection of the Niagara Escarpment.